Quantitative Biology

Authors and titles for October 2003

[1] arXiv:q-bio/0310001 [pdf, other]

Title: Comorbidity and Anticomorbidity: Autocognitive developmental disorders of structured psychosocial stress

Rodrick Wallace

Comments: 18 pages, 2 figures

Subjects: Neurons and Cognition (q-bio.NC); Tissues and Organs (q-bio.TO)

[2] arXiv:q-bio/0310002 [pdf, other]

Title: Deriving the respiratory sinus arrhythmia from the heartbeat time series using Empirical Mode Decomposition

R. Balocchi, D. Menicucci, E. Santarcangelo, L. Sebastiani, A. Gemignani, B. Ghelarducci, M. Varanini

Comments: 12 pages, 6 figures. Will be published on "Chaos, Solitons and Fractals"

Subjects: Tissues and Organs (q-bio.TO); Quantitative Methods (q-bio.QM)

[3] arXiv:q-bio/0310003 [pdf, other]

Title: Plant defense multigene families: I. Divergence of Fusarium solani-induced expression in Pisum and Lathyrus

Sandhya Tewari, Stuart M. Brown, Brian Fristensky

Comments: 13 pages, 6 figures arXiv reference added to first page; minor formatting changes

Subjects: Populations and Evolution (q-bio.PE)

[4] arXiv:q-bio/0310004 [pdf, other]

Title: Complexity and hierarchical game of life

Ivan Gotz, Isaak Rubinstein, Eugene Tsvetkov, Boris Zaltzman

Subjects: Populations and Evolution (q-bio.PE)

[5] arXiv:q-bio/0310005 [pdf, other]

Title: Structured psychosocial stress and therapeutic failure

Rodrick Wallace, Deborah Wallace

Comments: 18 pages, 4 figures

Subjects: Neurons and Cognition (q-bio.NC)

[6] arXiv:q-bio/0310006 [pdf, other]

Title: Dynamics of Fixation of Advantageous Mutations

Viviane M. de Oliveira, Paulo R. A. Campos

Comments: 13 pages

Subjects: Populations and Evolution (q-bio.PE)

[7] arXiv:q-bio/0310007 [pdf, other]

Title: Response kinetics of tethered bacteria to stepwise changes in nutrient concentration

Anna A. Chernova, Judith P. Armitage, Helen L. Packer, Philip K. Maini

Comments: 11 pages, 7 figures, in press in BioSystems

Subjects: Quantitative Methods (q-bio.QM)

[8] arXiv:q-bio/0310008 [pdf, other]

Title: The long reach of DNA sequence heterogeneity in diffusive processes

Michael Slutsky, Mehran Kardar, Leonid A. Mirny

Journal-ref: Phys. Rev. E 69, 061903 (2004)

Subjects: Biomolecules (q-bio.BM); Disordered Systems and Neural Networks (cond-mat.dis-nn); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

[9] arXiv:q-bio/0310009 [pdf, other]

Title: Resilience reconsidered: Case histories from disease ecology

Rodrick Wallace, Deborah Wallace

Comments: 21 pages, 8 figures

Subjects: Neurons and Cognition (q-bio.NC); Populations and Evolution (q-bio.PE)

[10] arXiv:q-bio/0310010 [pdf, other]

Title: The Yeast Cell-Cycle Network Is Robustly Designed

Fangting Li, Tao Long, Ying Lu, Qi Ouyang, Chao Tang

Comments: 24 pages, 7 figures, 3 tables; minor changes; journal version; higher resolution figures at this http URL

Journal-ref: PNAS 101, 4781 (2004).

Subjects: Molecular Networks (q-bio.MN); Statistical Mechanics (cond-mat.stat-mech); Cell Behavior (q-bio.CB)

[11] arXiv:q-bio/0310011 [pdf, other]

Title: Complex Independent Component Analysis of Frequency-Domain Electroencephalographic Data

Jorn Anemuller, Terrence J. Sejnowski, Scott Makeig

Comments: 21 pages, 11 figures. Added final journal reference, fixed minor typos

Journal-ref: Neural Networks, 16:1311-1323, 2003

Subjects: Quantitative Methods (q-bio.QM); Computational Engineering, Finance, and Science (cs.CE); Data Analysis, Statistics and Probability (physics.data-an); Neurons and Cognition (q-bio.NC)

[12] arXiv:q-bio/0310012 [pdf, other]

Title: Bioinformatics analysis of experimentally determined protein complexes in the yeast, S. cerevisiae

Zoltan Dezso, Zoltan N. Oltvai, Albert-Laszlo Barabasi

Comments: Supplementary Material available at this http URL

Subjects: Molecular Networks (q-bio.MN); Condensed Matter (cond-mat); Genomics (q-bio.GN)

[13] arXiv:q-bio/0310013 [pdf, other]

Title: Hydration Water Dynamics and Instigation of Protein Structural Relaxation

Daniela Russo, Greg Hura, Teresa Head-Gordon

Comments: 2 pages, 2 figures, Communication

Subjects: Biomolecules (q-bio.BM)

[14] arXiv:q-bio/0310014 [pdf, other]

Title: Auto-reverse nuclear migration in bipolar mammalian cells on micropatterned surfaces

B. Szabo, Zs. Kornyei, J. Zach, D. Selmeczi, G. Csucs, A. Czirok, T. Vicsek

Comments: Figures and supplemental videos: this http URL

Journal-ref: Cell Motility and the Cytoskeleton 59(1), 38-49 (2004)

Subjects: Cell Behavior (q-bio.CB)

[15] arXiv:q-bio/0310015 [pdf, other]

Title: How does connectivity between cortical areas depend on brain size? Implications for efficient computation

Jan Karbowski

Comments: brain, theoretical neuroanatomy, computational neuroanatomy, cortical areas, scaling, connectivity

Journal-ref: Journal of Computational Neuroscience 15, 347-356 (2003)

Subjects: Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM)

[16] arXiv:q-bio/0310016 [pdf, other]

Title: Cytokinesis: the initial linear phase crosses over to a multiplicity of non-linear endings

D. Biron, P. Libros, D. Sagi, D. Mirelman, E. Moses

Subjects: Cell Behavior (q-bio.CB)

[17] arXiv:q-bio/0310017 [pdf, other]

Title: Phase transition and selection in a four-species cyclic Lotka-Volterra model

Gyorgy Szabo, Gustavo Arial Sznaider

Comments: 4 pages, 5 figures

Journal-ref: Phys. Rev. E 69 (2004) 031911

Subjects: Populations and Evolution (q-bio.PE)

[18] arXiv:q-bio/0310018 [pdf, other]

Title: Fold-Hopf Bursting in a Model for Calcium Signal Transduction

Lutz Brusch, Wolfram Lorenz, Michal Or-Guil, Markus Bär, Ursula Kummer

Comments: 13 pages, 5 figures

Journal-ref: Z. Phys. Chem. 216, 487-497 (2002)

Subjects: Molecular Networks (q-bio.MN)

[19] arXiv:q-bio/0310019 [pdf, other]

Title: Complexity in the Immune System

Michael W. Deem

Comments: 25 pages, 12 figures

Subjects: Cell Behavior (q-bio.CB); Condensed Matter (cond-mat); Populations and Evolution (q-bio.PE)

[20] arXiv:q-bio/0310020 [pdf, other]

Title: Thermal denaturation and folding rates of single domain proteins: size matters

Mai Suan Li, D. K. Klimov, D. Thirumalai

Comments: 11 pages, 3 figures

Subjects: Biomolecules (q-bio.BM)

[21] arXiv:q-bio/0310021 [pdf, other]

Title: Communication on the letter: "Evolutionary Conservation of Motif Constituents in the Yeast Protein Interaction Network."

Stan Bumble

Comments: 2 pages

Subjects: Molecular Networks (q-bio.MN)

[22] arXiv:q-bio/0310022 [pdf, other]

Title: A covariance kernel for proteins

Marco Cuturi, Jean-Philippe Vert

Comments: 12 pages, 1 figure

Subjects: Genomics (q-bio.GN)

[23] arXiv:q-bio/0310023 [pdf, other]

Title: Asymmetry in the shapes of folded and denatured states of proteins

Ruxandra I. Dima, D. Thirumalai

Comments: 22 pages, 7 figures

Subjects: Biomolecules (q-bio.BM)

[24] arXiv:q-bio/0310024 [pdf, other]

Title: Evolutionary conservation of motif constituents within the yeast protein interaction network

S. Wuchty, Z.N. Oltvai, A.-L. Barabasi

Comments: 16 pages, 1 figure, 2 tables

Journal-ref: Nature Genetics, 35(2), 176-179, (2003)

Subjects: Genomics (q-bio.GN); Condensed Matter (cond-mat)

[25] arXiv:q-bio/0310025 [pdf, other]

Title: Pattern Excitation-Based Processing: The Music of The Brain

Lev Koyrakh

Comments: 15 pages, 7 figures, a reference corrected

Subjects: Neurons and Cognition (q-bio.NC); Neural and Evolutionary Computing (cs.NE); Biological Physics (physics.bio-ph)

[26] arXiv:q-bio/0310026 [pdf, other]

Title: Protein secondary structure prediction by combining hidden Markov models and sliding window scores

Wei-Mou Zheng

Comments: 8 pages, 1 figure, 2 tables

Subjects: Biomolecules (q-bio.BM)

[27] arXiv:q-bio/0310027 [pdf, other]

Title: Random model for RNA interference yields scale free network

Duygu Balcan, Ayse Erzan

Comments: 9 pages, 13 figures, submitted to Midterm Conference COSIN on ``Growing Networks and Graphs in Statistical Physics, Finance, Biology and Social Systems'', Rome, 1-5 September 2003

Subjects: Genomics (q-bio.GN)

[28] arXiv:q-bio/0310028 [pdf, other]

Title: Upstream Plasticity and Downstream Robustness in Evolution of Molecular Networks

Sergei Maslov, Kim Sneppen, Kasper Astrup Eriksen

Comments: 10 pages, 4 figures. Submitted to BMC evolutionary biology

Subjects: Molecular Networks (q-bio.MN); Populations and Evolution (q-bio.PE)

[29] arXiv:q-bio/0310029 [pdf, other]

Title: Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli

P. B. Warren, P. R. ten Wolde

Comments: 9 pages, 6 figs (4 colour)

Subjects: Molecular Networks (q-bio.MN); Genomics (q-bio.GN)

[30] arXiv:q-bio/0310030 [pdf, other]

Title: A graph model for the evolution of specificity in humoral immunity

L. E. Flores, E. J. Aguilar, V. C. Barbosa, L. A. V. de Carvalho

Journal-ref: Journal of Theoretical Biology 229 (2004), 311-325

Subjects: Cell Behavior (q-bio.CB)

[31] arXiv:q-bio/0310031 [pdf, other]

Title: The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes

P.G.Higgs, D.Jameson, H.Jow, M.Rattray

Comments: 20 pages, 6 figures. J. Mol. Evol. (in press)

Subjects: Populations and Evolution (q-bio.PE)

[32] arXiv:q-bio/0310032 [pdf, other]

Title: Localization and extinction of bacterial populations under inhomogeneous growth conditions

Anna L. Lin, Bernward A. Mann, Gelsy Torres-Oviedo, Bryan Lincoln, Josef Kas, Harry L. Swinney

Comments: 11 pages, 7 figures

Subjects: Populations and Evolution (q-bio.PE); Biological Physics (physics.bio-ph)

[33] arXiv:q-bio/0310033 [pdf, other]

Title: Pattern overlapping decomposition by Cumulative Local Cross-Correlation

Simon Kogan

Comments: 14 pages, 8 figures, 1 table

Subjects: Quantitative Methods (q-bio.QM); Biomolecules (q-bio.BM)

[34] arXiv:q-bio/0310034 [pdf, other]

Title: Protein secondary structure: Entropy, correlations and prediction

Gavin E. Crooks, Steven E. Brenner

Comments: 8 pages, 5 figures

Journal-ref: Bioinformatics 20:1603-1611 (2004)

Subjects: Biomolecules (q-bio.BM)

[35] arXiv:q-bio/0310035 [pdf, other]

Title: Why humans die -- an unsolved biological problem

Mark Ya. Azbel'

Comments: 4 pages, 3 figures

Subjects: Other Quantitative Biology (q-bio.OT); Biological Physics (physics.bio-ph); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[36] arXiv:q-bio/0310036 [pdf, other]

Title: "Junk" DNA as a genetic decoy

Joao Magueijo (Imperial College)

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

[37] arXiv:q-bio/0310037 [pdf, other]

Title: U(1)xU(1)xU(1) symmetry of the Kimura 3ST model and phylogenetic branching processes

J. D. Bashford, P. D. Jarvis, J. G. Sumner (U Tasmania), M. A. Steel (U Canterbury)

Comments: 9 pages, LaTeX, uses amsmath

Subjects: Populations and Evolution (q-bio.PE); Statistics Theory (math.ST); Quantitative Methods (q-bio.QM)

[38] arXiv:q-bio/0310038 [pdf, other]

Title: Plant defense multigene families: II Evolution of coding sequence and differential expression of PR10 genes in Pisum

S. Tewari, S. M. Brown, P. Kenyon, M. Balcerzak, B. Fristensky

Comments: 17 pages, 6 figures

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

[39] arXiv:q-bio/0310039 [pdf, other]

Title: Different ocular dominance map formation by influence of orientation columns in visual cortices

Myoung Won Cho, Seunghwan Kim

Comments: 4 pages, 4 figure

Subjects: Neurons and Cognition (q-bio.NC)

[40] arXiv:q-bio/0310040 [pdf, other]

Title: Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs

Davide Cora', Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo, Michele Caselle

Comments: 19 pages, 1 figure. Published version with several improvements. Supplementary material available from the authors

Journal-ref: BMC Bioinformatics. 2004 May 11;5(1):57

Subjects: Genomics (q-bio.GN)

[41] arXiv:q-bio/0310041 [pdf, other]

Title: Enhancement of the stability of genetic switches by overlapping upstream regulatory domains

Patrick B. Warren, Pieter Rein ten Wolde

Comments: 4 pages, 5 figures, RevTeX4

Subjects: Molecular Networks (q-bio.MN)

[42] arXiv:cond-mat/0310037 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Introduction to Statistical Physics outside Physics

Dietrich Stauffer

Comments: 6 pages of opinions, no simulations, draft for Ladek Zdroj proceedings

Subjects: Statistical Mechanics (cond-mat.stat-mech); Other Condensed Matter (cond-mat.other); Other Quantitative Biology (q-bio.OT)

[43] arXiv:cond-mat/0310038 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: The Complexity of Biological Ageing

Dietrich Stauffer

Comments: For Fractal 2004 proceedings, Vancouver; 12 pages of review including 6 figs

Subjects: Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)

[44] arXiv:cond-mat/0310091 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Functionals linear in curvature and statistics of helical proteins

V.V. Nesterenko, A. Feoli, G. Scarpetta

Comments: Contribution to the Proceedings of the International Conference "this http URL. Pomeranchuk and Physics at the Turn of Centuries," Moscow, January 24 - 28, 2003 (World Scientific, Singapore)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Biomolecules (q-bio.BM)

[45] arXiv:cond-mat/0310208 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Comments on evolution of cooperation: assortative encounters with selfknowledge

Pawel Sobkowicz

Comments: 19 pages, 6 figures

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Populations and Evolution (q-bio.PE)

[46] arXiv:cond-mat/0310242 (cross-list from cond-mat.soft) [pdf, other]

Title: Charge transport in l-DNA probed by conducting-AFM, and relationship with its structure

Thomas Heim, Dominique Deresemes, Dominique Vuillaume

Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Biomolecules (q-bio.BM)

[47] arXiv:cond-mat/0310266 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Comments on evolution of cooperation: evolutionary stability in enhanced Dove-Hawk model

Pawel Sobkowicz

Comments: 19 pages, 8 figures

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Populations and Evolution (q-bio.PE)

[48] arXiv:cond-mat/0310296 (cross-list from cond-mat.soft) [pdf, other]

Title: Onset of Shear Waves In A Bacterial Bath: A Novel Effect

Supurna Sinha

Comments: To appear in Fluctuation and Noise Letters

Subjects: Soft Condensed Matter (cond-mat.soft); Cell Behavior (q-bio.CB)

[49] arXiv:cond-mat/0310321 (cross-list from cond-mat.soft) [pdf, other]

Title: The pulling force of a single DNA molecule condensed by spermidine

R. Zhang, B. I. Shklovskii

Comments: 4 pages, 4 figures. Small change in the text, no change in results

Journal-ref: Physica A 349 (2005) 563

Subjects: Soft Condensed Matter (cond-mat.soft); Biomolecules (q-bio.BM)

[50] arXiv:cond-mat/0310372 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Immunization Dynamics on a 2-layer Network Model

Hang-Hyun Jo, Hie-Tae Moon, Seung Ki Baek (Korea Advanced Institute of Science and Technology)

Comments: 5 pages, 7 figures

Journal-ref: Physica A vol. 361, pp. 534-542 (2006)

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Populations and Evolution (q-bio.PE)